RNA polymerase eukaryote

The inhibitors of RNA polymerase, which generates RNA from DNA, inhibit a crucial step in gene expression. Inhibition of the eukaryotic form of RNA polymerase is used in cancer chemotherapy and is also an important experimental tool. For example, actinomy-cin D binds to the guanine residues in DNA and blocks the movement of the eukaryotic RNA polymerase. Specific inhibitors of bacterial RNA polymerase can be used as antibacterial agents. Most of these inhibitors like rifamycin bind to the prokaryotic enzyme. 

Ebright RH RNA polymerase structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 2000 304 S87. 

There are three eukaryotic RNA polymerases, distinguished by the particular types of RNA fhey produce ... 

Baer, B.W. and Rhodes, D. (1983) Eukaryotic RNA polymerase II binds to nucleosome cores from... 

Eick, D., Wedel,A. and Heumann, H. From initiation to elongation comparison of transcription by prokaryotic and eukaryotic RNA polymerases (1994) Trends Gen. 10, 292-296... 

S ATP -I- [DNA-directed eukaryotic RNA polymerase II subunit Ila] (<4> distinct from other protein phosphokinases, transfers about 20 phosphates to the heptapeptide repeats Pro-Thr-Ser-Pro-Ser-Tyr-Ser in C-terminal domain of MW 220000 subunit of RNA-polymerase II [7] <4> substrates are RNA-polymerase II subunits of wheat germ, soy bean, pea and human [7] phosphorylates predominantly Ser-residues [1-3,5,7] <1> kinase CTDKl almost exclusively phosphorylates Ser-residues [5] <1> kinase CTDK2 phosphorylates to a lesser extent Thr-resi-dues [1] <3-5> phosphorylates to a lesser extent Thr-residues [1,5,7] <1> phosphorylates Ser- and Thr-residues equally [6] <1,3,5> phosphorylates not Tyr-residues [1,6] <1> kinase CTDKl 33 mol phosphate per mol IIA-subunit [5] <1> kinase CTDK2 40-50 mol phosphate per mol IIA-subunit, i.e. 1 phosphate per heptapeptide repeat [5] <4> no substrate is GTP [7] <2,4> no substrates are CTP and UTP [3,7] <2> no substrates are dTTP and AMP-PNP [3] <4> no substrates are bovine serum albumin and calf thymus histone [7] <5> no substrate is phosvitin... 

Cisek, L.J. Corden, J.L. Purification of protein kinases that phosphorylate the repetitive carboxyl-terminal domain of eukaryotic RNA polymerase IL Methods Enzymol., 200, 301-325 (1991)... 

FIGURE 26-8 Common sequences in promoters recognized by eukaryotic RNA polymerase II. The TATA box is the major assembly point for the proteins of the preinitiation complexes of Pol II. The DNA is unwound at the initiator sequence (Inr), and the transcription start site is usually within or very near this sequence. In the Inr consensus sequence shown here, N represents any nucleotide Y, a pyrimidine nucleotide. Many additional sequences serve as binding sites for a wide variety of proteins that affect the activity of Pol II. These sequences are important in regulating Pol II promoters and vary greatly in type and... 

The sequences of eukaryotic promoters are more variable than their prokaryotic counterparts (see Fig. 26-8). The three eukaryotic RNA polymerases usually require an array of general transcription factors in order to bind to a promoter. Yet, as with prokaryotic gene expression, the basal level of transcription is determined by the effect of promoter sequences on the function of RNA polymerase and its associated transcription factors. 

As already noted, eukaryotic RNA polymerases have little or no intrinsic affinity for their promoters initiation of transcription is almost always dependent on the action of multiple activator proteins. One important reason for the apparent predominance of positive regulation seems obvious the storage of DNA within chromatin effectively renders most promoters inaccessible, so genes are normally silent in the absence of other regulation. The structure of chromatin affects access to some promoters more than others, but repressors that... 

The eukaryotic RNA polymerases are not inhibited by rifamycin, but RNA polymerases II and III are completely inhibited by the mushroom poison a-amanitin (see Box 28-B). Inhibitors of DNA gyrase (Chapter 27) also interfere with transcription as do chain terminators such as cordycepin (3 -deoxyadenosine) and related nucleosides. 

Eukaryotes Have Three Nuclear RNA Polymerases Eukaryotic RNA Polymerases Are Not Fully Functional by Themselves... 

Formation of the initiation complex for transcription for the three major classes of eukaryotic RNA polymerase Poll, PolII, and PolIII. Each polymerase consists of many subunits (not shown). In addition to the firmly bound subunits, a number of protein factors, called transcription factors (TFs), only associate with the polymerases at the initiation site for transcription. For all three polymerases some of... 

Rifampicin is a synthetic derivative of a naturally occurring antibiotic, rifamycin, that inhibits bacterial DNA-dependent RNA polymerase but not T7 RNA polymerase or eukaryotic RNA polymerases. It binds tightly to the ft subunit. Although it does not prevent promoter binding or formation of the first phosphodiester bond, it effectively prevents synthesis of longer RNA chains. It does not inhibit elongation when added after initiation has occurred. Another antibiotic, streptolydigin, also binds to the ft subunit it inhibits all bond formation. 

The basic mechanism of RNA synthesis by these eukaryotic RNA polymerases is the same as for the prokaryotic enzyme (see Topic G2), that is ... 

Each of the three eukaryotic RNA polymerases contains 12 or more subunits and so these are large complex enzymes. The genes encoding some of the subunits of each eukaryotic enzyme show DNA sequence similarities to genes encoding subunits of the core enzyme (a2PP ) of E. coli RNA polymerase (see Topic G2). However, four to seven other subunits of each eukaryotic RNA polymerase are unique in that they show no similarity either with bacterial RNA polymerase subunits or with the subunits of other eukaryotic RNA polymerases. 

The rRNA promoter consists of a core element which straddles the transcriptional start site (designated as position +1) from residues -31 to +6 plus an upstream control element (UCE) about 50-80 bp in size and located about 100 bp upstream from the start site (i.e. at position -100 Fig. 4b). A transcription factor called upstream binding factor (UBF) binds both to the UCE as well as to a region next to and overlapping with the core element. Interestingly, TATA box binding protein (TBP see Topic G6), also binds to the rRNA promoter (in fact, TBP is required for initiation by all three eukaryotic RNA polymerases). The UBF and TBP transcription factors interact with each other and with RNA Pol I to form a transcription initiation complex. The RNA Pol I then transcribes... 

In eukaryotes, the tRNA genes exist as multiple copies and are transcribed by RNA polymerase III (RNA Pol III). As in prokaryotes, several tRNAs may be transcribed together to yield a single pre-tRNA molecule that is then processed to release the mature tRNAs. The promoters of eukaryotic tRNA genes are unusual in that the transcriptional control elements are located downstream (i.e. on the 3 side) of the transcriptional start site (at position +1). In fact they lie within the gene itself. Two such elements have been identified, called the A box and B box (Fig. 3). Transcription of the tRNA genes by RNA Pol III requires transcription factor IIIC (TFIIIC) as well as TFIIIB. THIIC binds to the A and B boxes whilst TFIIIB binds upstream of the A box. TFIIIB contains three subunits, one of which is TBP (TATA binding protein), the polypeptide required by all three eukaryotic RNA polymerases. 

Eukaryotic transcription uses three distinct RNA polymerases, which are specialized for different RNAs. RNA polymerase I makes Ribosomal RNAs, RNA polymerase II makes messenger RNAs, and RNA polymerase III makes small, stable RNAs such as transfer RNAs and 5S ribosomal RNA. Eukaryotic RNA polymerases are... 

No. Eukaryotic RNA polymerases have been isolated from many tissues, and in all cases, three distinct enzymes have been found in the nucleus. All contain a number of polypeptide subunits and are complex in structure, RNA polymerase I is known to be involved specifically in the transcription of rRNA genes. RNA polymerase II gives rise to transcripts that are subsequently processed to yield mRNA. RNA polymerase 111 is responsible for the transcription of the tRNA genes and a small ribosomal RNA gene that yields a species called 55 RNA. The three polymerases are distinguishable from one another by their differential sensitivity to the drug a-amanitin (the toxic principle of the mushroom Amanita phalloides), which does not affect bacterial RNA polymerase. RNA polymerase... 

The role of the various subunits of the eukaryotic RNA polymerases has not yet been defined, but presumably there are subunits equivalent to the bacterial <7 factor involved in the recognition of promoter sites. As with bacterial promoters, homologies upstream of the start point of transcription have been identified. 

Yes. Examples are rifampicin and streptolydigin, which bind only to bacterial RNA polymerase and block its action a-amanitin binds only to eukaryotic RNA polymerase II and, to a lesser extent, to RNA polymerase III to block their actions. 

Is it possible that a-amanitin exerts its inhibitory effect on certain eukaryotic RNA polymerases by interfering with the availability of the substrates ... 

Clear evidence exists to prove that ansamycins such as rifampicin have no effect on eukaryotic RNA polymerases, be they of nuclear, mitochondrial or chloroplastic... 

Bucher, P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol 212,563-78. 

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